☰ Navigation Tabs
Crystal structure of retroviral protease-like domain of Ddi1 from Cryptosporidium hominis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7D66
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6 291 0.1 M MES-sodium hydroxide (pH 6.0), 30% polyacrylate sodium salt and 10% ethanol
Crystal Properties Matthews coefficient Solvent content 3.19 61.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.559 α = 90 b = 81.559 β = 90 c = 142.181 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2020-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.9918 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 63.26 100 0.99 11.1 7.5 4686
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.8 100 0.84 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7D66 2.8 47.439 4683 222 99.915 0.186 0.1836 0.1852 0.2338 0.2342 85.776
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 3.332 1.666 3.332 -10.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.993 r_lrange_it 17.763 r_dihedral_angle_3_deg 16.27 r_scangle_it 15.591 r_scbond_it 11.637 r_mcangle_it 11.21 r_mcbond_it 7.912 r_dihedral_angle_1_deg 6.679 r_dihedral_angle_4_deg 2.96 r_angle_refined_deg 1.497
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.993 r_lrange_it 17.763 r_dihedral_angle_3_deg 16.27 r_scangle_it 15.591 r_scbond_it 11.637 r_mcangle_it 11.21 r_mcbond_it 7.912 r_dihedral_angle_1_deg 6.679 r_dihedral_angle_4_deg 2.96 r_angle_refined_deg 1.497 r_nbtor_refined 0.323 r_symmetry_nbd_refined 0.298 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.111 r_chiral_restr 0.104 r_bond_refined_d 0.006 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 852 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing